The quantitative assay of nucleic acids is of considerable importance in basic biological research as well as in fields such as clinical microbiology. The real-time polymerase chain reaction (real-time PCR) process was developed in the mid 1990's to improve the original PCR process in a way that provides reliable, accurate quantitative measurements of the number of copies of any target DNA in the sample. In a real-time PCR, fluorogenic probes that are only active when bound to target DNA are added to the PCR buffer solution. These fluorogenic probes are single strands of DNA, with a middle portion having a sequence of nucleotides that is complementary to the target DNA. On either side of this middle portion, are extension nucleotide sequences that are complementary to each other, so that an unattached probe will fold onto itself in a hairpin configuration. The fluorogenic probe has a fluorescent molecule at one end, and a fluorescence quenching molecule at the other end. An unattached, folded probe has a fluorescing and a quenching molecule adjacent to each other, and consequently no fluorescent light is emitted when the unattached probe is illuminated. When the fluorogenic probe is attached to its target DNA, however, it is unfolded, with the fluorescing and quenching molecules separated from each other. When the attached probe is illuminated with the appropriate wavelength of light, the fluorescent molecule emits fluorescent light. By providing sufficient fluorogenic probes for a particular target DNA, and measuring the fluorescence from the bound probes at each stage of the PCR, the number of amplicons at each stage of the reaction can be measured. This measurement can be used to very accurately determine the number of copies of the DNA in the initial sample because of a straight line relationship between the fractional number of cycles for the number of amplicons to reach a pre-determined threshold and the logarithm of the number of copies in the initial sample.